Remove PEtab v2 mapping-table/YAML handling from petab.v1

[dweindl]

petab.v1 had accumulated v2-only functionality that was implemented directly in the v1 package instead of v2: the entity mapping table, extensions_config, and a deprecated v2-format YAML loading branch in Problem.from_yaml. The v1 spec has no mapping table, no extensions, and no model_files/language keys, so none of this belongs in petab.v1.

This PR:

• Moves the mapping-table implementation to petab.v2.mapping (v2 no longer imports it from v1).
• Strips mapping_df/extensions_config threading out of v1's Problem, lint, parameters, observables, and parameter_mapping modules.
• Makes Problem.from_yaml raise a clear error for v2-format YAML instead of a deprecation warning followed by a load path that no longer works.

Non-SBML model support (PySB, BNGL) in petab.v1.models is left untouched; that's a separate follow-up.

🤖 Generated with Claude Code

[codecov-commenter]

Codecov Report

❌ Patch coverage is 83.33333% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 76.43%. Comparing base (2610499) to head (d52aba4).

Files with missing lines	Patch %	Lines
petab/v1/problem.py	66.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #524      +/-   ##
==========================================
+ Coverage   76.15%   76.43%   +0.27%     
==========================================
  Files          67       67              
  Lines        7528     7477      -51     
  Branches     1342     1326      -16     
==========================================
- Hits         5733     5715      -18     
+ Misses       1294     1272      -22     
+ Partials      501      490      -11     

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[dilpath]

Will it break someone's workflow/should there be a deprecation period?

[dweindl]

Will it break someone's workflow/should there be a deprecation period?

Hard to tell, but I don't think so. At least for the v2 constants in petab.v1.C, deprecation comments were added 2 years ago (dweindl@7fd4498).

[dweindl]

Will it break someone's workflow

I think there is still some amici code (tracked at AMICI-dev/AMICI#3305) relying on that. Pypesto is only indirectly affected through amici. Will wait until that's resolved.